30 October -3 November 2023

To foster international participation, this course will be held online

Epigenetic studies on DNA methylation are now possible to do at the nucleotide level genome-wide also in non-model organisms. In this course, we will introduce the different available approaches for obtaining and analysing DNA methylation data, including bisulfite sequencing (BS-seq) with Ilumina and long reads with PacBio and Oxford Nanopore. We will cover all necessary steps to obtain methylation information from high throughput data to statistical analyses used to identify differentially methylated sites and regions. The data will be interpreted in terms of their biological importance in the field of ecology and evolution.

The course will be delivered over the course of five days. Each day will include an introductory lecture with class discussion of key concepts. The remainder of each day will consist of practical hands-on sessions. These sessions will involve a combination of both mirroring exercises with the instructor to demonstrate a skill as well as applying these skills on your own to complete individual exercises.

This course is aimed at researchers and technical workers who are or who will be generating and/or analyzing DNA methylation from reduced representation or whole genome bisulfite sequencing data from IIlumina, PacBio data or Nanopore data. Examples demonstrated in this course will involve primarily non-model organisms with a draft reference genome available and examples of applications of this data type for different purposes will be covered.

Monday - DNA methylation analyses with short reads (Illumina BS-seq) - 2-8 pm Berlin time

Lecture 1
•    DNA methylation in the field of Ecology and Evolution: what are the patterns of diversity of DNA methylation between species, across populations and within the genome?
•    WGBS and RRBS protocols and sequence format. General processing of bisulfite data with a reference genome

Lab 1 (Part 1)
•    Introduction to files (header etc)
•    Quality Check (QC)
•    Genome prep, alignment and methylation calling, mbias using RRBS data (reference genome, Bismark)

Instructors